{"id":8925,"date":"2013-01-05T18:22:44","date_gmt":"2013-01-05T18:22:44","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=8925"},"modified":"2013-01-08T13:13:02","modified_gmt":"2013-01-08T13:13:02","slug":"%cf%80-hydrogen-bonds-as-a-function-of-ring-size","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","title":{"rendered":"\u03c0-hydrogen bonds as a function of ring size."},"content":{"rendered":"
\n

A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)\/H-O \u03c3* NBO interaction in that ring,\u00a0indicated<\/a> a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the \u03c0-electrons of an alkene as the electron donor.<\/p>\n

\"pi-hbond\"<\/p>\n\n\n\n\n\n\n\n
n\u00a0<\/th>\nE(2), kcal\/mol\u00a0<\/th>\nO…H length, \u00c5\u00a0<\/th>\nAngle,\u00b0<\/th>\n<\/tr>\n
2<\/td>\n0.84<\/a><\/td>\n2.54, 2.75<\/td>\n107.4, 126.7<\/td>\n<\/tr>\n
3<\/td>\n1.37<\/a><\/td>\n2.35, 2.92<\/td>\n133.1, 152.9<\/td>\n<\/tr>\n
4<\/td>\n2.04<\/a><\/td>\n2.45, 2.63<\/td>\n139.1, 144.5<\/td>\n<\/tr>\n
5<\/td>\n1.89<\/a><\/td>\n2.56, 2.63<\/td>\n152.2, 138.9<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

The E(2) interaction energies between the NBO filled \u03c0-orbital localised to the alkene and the H-O \u03c3* are significantly smaller than for O(Lp) as donors. The energy gap between the donor and acceptor\u00a0orbitals is smaller for\u00a0\u03c0 (\u0394E=0.919) than for the O…HO (0.969 au) and if one can compare these values across different localisations, then the finger must point to reduced overlap as the more probable explanation.<\/p>\n

\"7pi\"

NBO interaction for 7-ring H-bond. Click for 3D.<\/p><\/div>\n

So does that mean that \u03c0 bonds do not form? Well take a look at this molecule<\/a>:[1]<\/a><\/span>, which exhibits one example of a\u00a0\u03c0-bond and one of a conventional O…HO bond. E(2) for the\u00a0\u03c0 interaction is now 6.6 kcal\/mol, and the C…H distance is 2.16\u00c5 (calc, 2.1-2.2\u00c5\u00a0at its shortest, obs).\u00a0<\/p>\n

\"WAK\"<\/p>\n

\"7pi\"

NBO interaction for 7-ring H-bond. Click for 3D.<\/p><\/div>\n

There are probably several reasons for this.<\/p>\n

    \n
  1. The geometry of the scaffold enforces close proximity of the alkene and the OH group. The geometry of the scaffold results in a greater overlap of the C=C \u03c0 and H-O\u00a0\u03c3*\u00a0NBOs.\u00a0Recollect however the H…H distance in cis-butene<\/a>, a proximity that was enforced by other effects and which I argued was NOT a chemical bond.<\/li>\n
  2. The energy gap between filled and empty NBOs is slightly reduced from 0.919 to to 0.902 au.<\/li>\n
  3. This in turn may arise because the acceptor strength of the H-O\u00a0\u03c3* is enhanced by a knock-on effect by an additional conventional hydrogen bond the O (Lp) on this oxygen is forming to a H-O of a second molecular unit.<\/li>\n<\/ol>\n

    So we may conclude that whilst strong\u00a0\u03c0 H-O hydrogen bonds can be observed, they arise for the molecule shown above from a co-operation of several affects associated with the specific environment, rather than the intrinsic propensity of this type of H-bond to form strong interactions. But one more surprise (perhaps, or possibly just a further insight). The NCI (non-covalent-interactions) surface.<\/p>\n

    \"Non-covelent-interactions

    Non-covalent-interactions (NCI) surface. Click for 3D.<\/p><\/div>\n

    This maps the character of the (electron) density gradients, and shows up as blue (attractive) and red (repulsive). Four different regions show up as blue. Arrow 1 is our\u00a0C=C \u03c0…H-O bond. Note how adjacent to the blue region is a green-yellow one, indicating weak repulsions there (this proximity of both attractive and repulsive regions of the density was suggested to account for the confusion surrounding the \u00a0H…H interaction in\u00a0cis-butene<\/a>). Blue on its own however occurs in the region indicated by \u00a0arrow \u00a02. In this, the conventional \u00a0O…H-O attraction has no associated repulsion, which may also be an explanation for why such bonds are far more common. But the surprise is arrow 3, which suggests attractive back donation from the O(Lp) to the \u03c0* empty orbital (E(2) 1.4 kcal\/mol) \u00a0and arrow 4 indicates an attractive donation from the C=C\u00a0\u03c0 to the \u00a0C=O\u00a0\u03c0* (E(2) = 0.6 kcal\/mol). In this particularly rigid system, all these are largely enforced by the atom-scaffold. but it does all show how we often miss noticing the weaker interactions in molecules.<\/p>\n

    References<\/h2>\n
    1. M. Etzkorn, S.D. Smeltz-Zapata, T.B. Meyers, X. Yu, and M. Gerken, \"From the anti-tricyclo[4.2.1.12,5]deca-3,7-diene framework to 4,5,6,7-tetrachloro-isoindenone derivatives\", Tetrahedron Letters<\/i>, vol. 51, pp. 6075-6077, 2010. https:\/\/doi.org\/10.1016\/j.tetlet.2010.09.045<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)\/H-O \u03c3* NBO interaction in that ring,\u00a0indicated a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the \u03c0-electrons of an alkene as the electron donor. n\u00a0 E(2), kcal\/mol\u00a0 O…H length, […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[212],"ppma_author":[2661],"class_list":["post-8925","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-energy-gap"],"yoast_head":"\n\u03c0-hydrogen bonds as a function of ring size. - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c0-hydrogen bonds as a function of ring size. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)\/H-O \u03c3* NBO interaction in that ring,\u00a0indicated a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the \u03c0-electrons of an alkene as the electron donor. n\u00a0 E(2), kcal\/mol\u00a0 O…H length, […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-01-05T18:22:44+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-01-08T13:13:02+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-hbond.svg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"\u03c0-hydrogen bonds as a function of ring size. - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","og_locale":"en_GB","og_type":"article","og_title":"\u03c0-hydrogen bonds as a function of ring size. - Henry Rzepa's Blog","og_description":"A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)\/H-O \u03c3* NBO interaction in that ring,\u00a0indicated a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the \u03c0-electrons of an alkene as the electron donor. n\u00a0 E(2), kcal\/mol\u00a0 O…H length, […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","og_site_name":"Henry Rzepa's Blog","article_published_time":"2013-01-05T18:22:44+00:00","article_modified_time":"2013-01-08T13:13:02+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-hbond.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"\u03c0-hydrogen bonds as a function of ring size.","datePublished":"2013-01-05T18:22:44+00:00","dateModified":"2013-01-08T13:13:02+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925"},"wordCount":587,"commentCount":4,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-hbond.svg","keywords":["energy gap"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","name":"\u03c0-hydrogen bonds as a function of ring size. - 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Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors. FIMNEU The NCI surface for\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"FIMNEU. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16573,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16573","url_meta":{"origin":8925,"position":1},"title":"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face?","author":"Henry Rzepa","date":"June 22, 2016","format":false,"excerpt":"I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here\u00a0I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and\u00a0OH or NH groups. I start by defining a benzene ring with a centroid.\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"aromatic-pi-query","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/aromatic-pi-query-1-e1466580253270.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":8925,"position":2},"title":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding.","author":"Henry Rzepa","date":"March 10, 2017","format":false,"excerpt":"A few years back, I did a post about the Pirkle reagent and the unusual \u03c0-facial hydrogen bonding structure it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/142-1024x770.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":8860,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8860","url_meta":{"origin":8925,"position":3},"title":"Hydrogen bond strength as a function of ring size.","author":"Henry Rzepa","date":"January 3, 2013","format":false,"excerpt":"One frequently has to confront the question: will a hydrogen bond form between a suitable donor (lone pair or \u03c0) and an acceptor? One of the factors to be taken into consideration for hydrogen bonds which are part of a cycle is the ring size. Here I explore one way\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":4893,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4893","url_meta":{"origin":8925,"position":4},"title":"Some fun with no-go areas of chemistry: cyclobutadiene.","author":"Henry Rzepa","date":"September 18, 2011","format":false,"excerpt":"Organic chemistry has some no-go areas, where few molecules dare venture. One of them is described by a concept known as anti-aromaticity. Whereas aromatic molecules are favoured species, their anti-equivalent is avoided. I previously illustrated this (H\u00fcckel rule) with cyclopropenium anion. Now I take a look at cyclobutadiene, for which\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/cbdzw.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18755,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18755","url_meta":{"origin":8925,"position":5},"title":"One more WATOC 2017 Report.","author":"Henry Rzepa","date":"August 31, 2017","format":false,"excerpt":"Conferences can be intense, and this one is no exception. After five days, saturation is in danger of setting in. But before it does, I include two more (very) brief things I have learnt. Sason Shaik introduced a theme he first investigated years ago, but for which no experiment had\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8925","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=8925"}],"version-history":[{"count":26,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8925\/revisions"}],"predecessor-version":[{"id":8954,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8925\/revisions\/8954"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=8925"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=8925"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=8925"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=8925"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}